It sounds like you want to change the size of the Away3D viewport that you have loaded as part of a separate SWF? What you really need to do is make sure that you set the width/height properties of the View3D instance, not of the root of the other SWF. This means that you need to find a way to access the View3D of your loaded SWF, or by overriding the width/height setters in your loaded SWF’s document class and set the width/height of your View3D instance in there.
Bottom line is, the View3D instance is just a “proxy” object that acts a little like a display object, but the actual rendering is happening behind everything else directly on the stage (via Stage3D). So some rules that generally apply to display objects are not applicable here.
To recap, make sure you set the width and height of your View3D instance, either through accessing it directly, or through some method or properties on your loaded SWF’s document class.